IMO the 3-band EQ in the Core will clutter the options menu with extra features that have nothing to do with Genesis emulation.
Extra audio filtering or effects have their respected place but they should not be part of any core unless it is directly related to the emulation, especially when Retroarch has such vast external filtering/shaders support.
Why not a 31-band EQ or Parametric EQ or CRT-Royale in GenPlusGX then?
IMHO skip the 3-band EQ, it does not have its place in GenPlusGX,
If you ask me, having a MONO feature in GenPlusGX is much more important than EQ because Model1 had only mono sound from the back of the console and many TVs back then only had one speaker.
As for sampling rate conversion, why not let GenPlusGX follow the user set sampling rate in Retroarch? Most keep it at 48kHz anyway.
Nestopia runs at 48000Hz default and I don’t see any brickwall filtering behavior like in GenPlusGX.